{"id":"https://openalex.org/W2953299159","doi":"https://doi.org/10.1186/s13637-016-0044-y","title":"A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB","display_name":"A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in MATLAB","publication_year":2016,"publication_date":"2016-08-08","ids":{"openalex":"https://openalex.org/W2953299159","doi":"https://doi.org/10.1186/s13637-016-0044-y","mag":"2953299159","pmid":"https://pubmed.ncbi.nlm.nih.gov/27547217"},"language":"en","primary_location":{"id":"doi:10.1186/s13637-016-0044-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0044-y","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0044-y","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0044-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045112901","display_name":"Shriprakash Sinha","orcid":"https://orcid.org/0000-0001-7027-5788"},"institutions":[{"id":"https://openalex.org/I4210121466","display_name":"Indian Institute of Technology Bhilai","ror":"https://ror.org/02sscsx71","country_code":"IN","type":"education","lineage":["https://openalex.org/I4210121466"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Shriprakash Sinha","raw_affiliation_strings":["104-Madhurisha Heights Phase 1, Risali, Bhilai, 490006 India","104-Madhurisha Heights Phase 1, Risali, Bhilai, 490006, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"104-Madhurisha Heights Phase 1, Risali, Bhilai, 490006 India","institution_ids":[]},{"raw_affiliation_string":"104-Madhurisha Heights Phase 1, Risali, Bhilai, 490006, India","institution_ids":["https://openalex.org/I4210121466"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045112901"],"corresponding_institution_ids":["https://openalex.org/I4210121466"],"apc_list":null,"apc_paid":null,"fwci":0.3417,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69781085,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"2017","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9919000267982483,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7997338771820068},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4695205092430115},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.44196322560310364},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4189325273036957},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.40791600942611694},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.34080973267555237},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3108808994293213},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24701836705207825}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7997338771820068},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4695205092430115},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.44196322560310364},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4189325273036957},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.40791600942611694},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.34080973267555237},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3108808994293213},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24701836705207825}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13637-016-0044-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0044-y","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0044-y","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},{"id":"pmid:27547217","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27547217","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP journal on bioinformatics & systems biology","raw_type":null},{"id":"pmh:oai:europepmc.org:3948961","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4977324","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13637-016-0044-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13637-016-0044-y","pdf_url":"https://bsb-eurasipjournals.springeropen.com/track/pdf/10.1186/s13637-016-0044-y","source":{"id":"https://openalex.org/S22696228","display_name":"EURASIP Journal on Bioinformatics and Systems Biology","issn_l":"1687-4145","issn":["1687-4145","1687-4153"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EURASIP Journal on Bioinformatics and Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320251","display_name":"Royal Society of Chemistry","ror":"https://ror.org/025sbr097"},{"id":"https://openalex.org/F4320321012","display_name":"Technische Universiteit Delft","ror":"https://ror.org/02e2c7k09"},{"id":"https://openalex.org/F4320328786","display_name":"Norwegian Biodiversity Information Centre","ror":"https://ror.org/04jnzhb65"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953299159.pdf","grobid_xml":"https://content.openalex.org/works/W2953299159.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1651154209","https://openalex.org/W1967073403","https://openalex.org/W1968918164","https://openalex.org/W1984831467","https://openalex.org/W1987705498","https://openalex.org/W1988545801","https://openalex.org/W1992186965","https://openalex.org/W1993748871","https://openalex.org/W1997452920","https://openalex.org/W2001505418","https://openalex.org/W2002698073","https://openalex.org/W2007471837","https://openalex.org/W2015934446","https://openalex.org/W2017641880","https://openalex.org/W2022623685","https://openalex.org/W2026392519","https://openalex.org/W2043046936","https://openalex.org/W2046387526","https://openalex.org/W2048005397","https://openalex.org/W2049202209","https://openalex.org/W2057199920","https://openalex.org/W2061280979","https://openalex.org/W2070978045","https://openalex.org/W2073307618","https://openalex.org/W2075907707","https://openalex.org/W2076745770","https://openalex.org/W2100603120","https://openalex.org/W2107648723","https://openalex.org/W2109162004","https://openalex.org/W2110355953","https://openalex.org/W2113155233","https://openalex.org/W2117625122","https://openalex.org/W2119394710","https://openalex.org/W2129597370","https://openalex.org/W2133289216","https://openalex.org/W2142117690","https://openalex.org/W2143158512","https://openalex.org/W2147377553","https://openalex.org/W2150000725","https://openalex.org/W2154471160","https://openalex.org/W2159080219","https://openalex.org/W2167553081","https://openalex.org/W2167638513","https://openalex.org/W2320015545","https://openalex.org/W2411921399","https://openalex.org/W2611370172","https://openalex.org/W2979006918","https://openalex.org/W3083113686","https://openalex.org/W3133236490","https://openalex.org/W4230900352","https://openalex.org/W4233749076","https://openalex.org/W4299515571"],"related_works":["https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W4393677513","https://openalex.org/W4390832911","https://openalex.org/W829257147","https://openalex.org/W4385302116","https://openalex.org/W3081389670","https://openalex.org/W2150344375"],"abstract_inverted_index":{"Simulation":[0],"study":[1,176],"in":[2,14,32,75,93,136,168,248],"systems":[3],"biology":[4],"involving":[5],"computational":[6,69,98,189],"experiments":[7,99],"dealing":[8],"with":[9,103,205],"Wnt":[10,72],"signaling":[11,73],"pathways":[12],"abound":[13],"literature":[15,154],"but":[16],"often":[17],"lack":[18],"a":[19,76,137,183,206,217],"pedagogical":[20],"perspective":[21],"that":[22,100],"might":[23,46,90],"ease":[24],"the":[25,39,42,59,95,106,119,123,134,143,146,149,158,161,169,174,180,211,233,249],"understanding":[26,94],"of":[27,41,61,71,97,105,122,140,148,160,216,221],"beginner":[28],"students":[29],"and":[30,109,132,145,164,191,194,239],"researchers":[31],"transition,":[33],"who":[34],"intend":[35],"to":[36,49,68,209],"work":[37],"on":[38,58,237],"modeling":[40,70],"pathway.":[43],"This":[44],"paucity":[45],"happen":[47],"due":[48],"restrictive":[50],"business":[51],"policies":[52],"which":[53],"enforce":[54],"an":[55],"unwanted":[56],"embargo":[57],"sharing":[60],"important":[62],"scientific":[63],"knowledge.":[64],"A":[65],"tutorial":[66],"introduction":[67],"pathway":[74],"human":[77],"colorectal":[78],"cancer":[79],"dataset":[80],"using":[81,197],"static":[82],"Bayesian":[83,113],"network":[84,114,170],"models":[85,111],"is":[86,101,155,171,177,186,224],"provided.":[87],"The":[88,116,201],"walkthrough":[89],"aid":[91],"biologists/informaticians":[92],"design":[96],"interleaved":[102],"exposition":[104],"Matlab":[107,222],"code":[108,235],"causal":[110],"from":[112,153],"toolbox.":[115],"manuscript":[117,202],"elucidates":[118],"coding":[120],"contents":[121],"advance":[124],"article":[125],"by":[126],"Sinha":[127],"(Integr.":[128],"Biol.":[129],"6:1034\u20131048,":[130],"2014)":[131],"takes":[133],"reader":[135],"step-by-step":[138],"process":[139],"how":[141],"(a)":[142],"collection":[144],"transformation":[147],"available":[150,226],"biological":[151,166,184],"information":[152],"done,":[156],"(b)":[157],"integration":[159],"heterogeneous":[162],"data":[163],"prior":[165],"knowledge":[167],"achieved,":[172],"(c)":[173],"simulation":[175],"designed,":[178],"(d)":[179],"hypothesis":[181],"regarding":[182],"phenomena":[185],"transformed":[187],"into":[188],"framework,":[190],"(e)":[192],"results":[193],"inferences":[195],"drawn":[196],"d-connectivity/separability":[198],"are":[199],"reported.":[200],"finally":[203],"ends":[204],"programming":[207],"assignment":[208],"help":[210],"readers":[212],"get":[213],"hands-on":[214],"experience":[215],"perturbation":[218],"project.":[219],"Description":[220],"files":[223],"made":[225],"under":[227],"GNU":[228],"GPL":[229],"v3":[230],"license":[231],"at":[232],"Google":[234],"project":[236],"https://code.google.com/p/static-bn-for-wnt-signaling-pathway":[238],"https:":[240],"//sites.google.com/site/shriprakashsinha/shriprakashsinha/projects/static-bn-for-wnt-signaling-pathway":[241],".":[242],"Latest":[243],"updates":[244],"can":[245],"be":[246],"found":[247],"latter":[250],"website.":[251]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}